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 Vol 46: Identity-by-descent genomic selection using selective and sparse genotyping.


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This article is from Genetics, Selection, Evolution : GSE, volume 46.AbstractBackground: Genomic selection methods require dense and widespread genotyping data, posing a particular challenge if both sexes are subject to intense selection e.g., aquaculture species. This study focuses on alternative low-cost genomic selection methods IBD-GS that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis. Our aim was to evaluate the potential of these methods in selection programs for continuous traits measured on sibs of selection candidates in a typical aquaculture breeding population. Methods: Phenotypic and genomic data were generated by stochastic simulation, assuming low to moderate heritabilities 0.10 to 0.30 for a Gaussian trait measured on sibs of the selection candidates in a typical aquaculture breeding population that consisted of 100 families 100 training animals and 20 selection candidates per family. Low-density marker genotype data ~ 40 markers per Morgan were used to trace genomic identity-by-descent relationships. Genotyping was restricted to selection candidates from 30 phenotypically top-ranking families and varying fractions of their phenotypically extreme training sibs. All phenotypes were included in the genetic analyses. Classical pedigree-based and IBD-GS models were compared based on realized genetic gain over one generation of selection. Results: Genetic gain increased substantially 13 to 32% with IBD-GS compared to classical selection and was greatest with higher heritability. Most of the extra gain from IBD-GS was obtained already by genotyping the 5% phenotypically most extreme sibs within the pre-selected families. Additional genotyping further increased genetic gains, but these were small when going from genotyping 20% of the extremes to all phenotyped sibs. The success of IBD-GS with sparse and selective genotyping can be explained by the fact that within-family haplotype blocks are accurately traced even with low-marker densities and that most of the within-family variance for normally distributed traits is captured by a small proportion of the phenotypically extreme sibs. Conclusions: IBD-GS was substantially more effective than classical selection, even when based on very few markers and combined with selective genotyping of small fractions of the population. The study shows that low-cost GS programs can be successful by combining sparse and selective genotyping with pedigree and linkage information.



Autor: ?degard, J?rgen; Meuwissen, Theo HE

Fuente: https://archive.org/







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